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Chlorine in PDB 3thd: Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin

Enzymatic activity of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin

All present enzymatic activity of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin:
3.2.1.23;

Protein crystallography data

The structure of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin, PDB code: 3thd was solved by U.Ohto, T.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.29 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.792, 115.996, 140.327, 90.00, 92.22, 90.00
R / Rfree (%) 19.8 / 22.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin (pdb code 3thd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin, PDB code: 3thd:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3thd

Go back to Chlorine Binding Sites List in 3thd
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl801

b:7.5
occ:1.00
 OG A:SER54 3.1 10.1 1.0
NE2 A:HIS56 3.2 7.9 1.0
NH2 A:ARG121 3.2 8.1 1.0
NE A:ARG121 3.4 8.8 1.0
CB A:SER54 3.6 9.3 1.0
CG A:GLN81 3.7 10.1 1.0
O A:GLN81 3.7 9.4 1.0
CZ A:ARG121 3.8 8.7 1.0
CD2 A:HIS56 3.8 7.6 1.0
CA A:THR82 3.8 8.7 1.0
C A:GLN81 3.8 9.5 1.0
OE1 A:GLN81 3.9 11.4 1.0
N A:THR82 3.9 9.0 1.0
C A:THR82 3.9 8.9 1.0
CD2 A:TYR83 4.1 7.5 1.0
N A:TYR83 4.1 8.7 1.0
CE1 A:TYR306 4.1 8.5 1.0
CB A:GLN81 4.2 10.0 1.0
CE2 A:TYR83 4.2 7.2 1.0
CD1 A:TYR306 4.2 8.9 1.0
CD A:GLN81 4.2 11.0 1.0
CG A:TYR83 4.3 7.6 1.0
O A:THR82 4.4 9.5 1.0
CA A:SER54 4.4 9.3 1.0
CE1 A:HIS56 4.4 8.3 1.0
CZ A:TYR83 4.6 7.7 1.0
CD A:ARG121 4.6 9.1 1.0
CA A:GLN81 4.7 9.9 1.0
CD1 A:TYR83 4.7 7.6 1.0
CE1 A:TYR83 4.8 8.0 1.0
CG A:ARG121 4.8 8.8 1.0
CB A:TYR83 4.9 7.7 1.0
CA A:TYR83 4.9 8.1 1.0

Chlorine binding site 2 out of 4 in 3thd

Go back to Chlorine Binding Sites List in 3thd
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl801

b:5.6
occ:1.00
 OG B:SER54 3.0 8.2 1.0
NE2 B:HIS56 3.2 7.3 1.0
NH2 B:ARG121 3.2 8.5 1.0
NE B:ARG121 3.4 10.3 1.0
CB B:SER54 3.7 8.0 1.0
CG B:GLN81 3.7 8.8 1.0
O B:GLN81 3.7 8.2 1.0
NE2 B:GLN81 3.7 9.0 1.0
CZ B:ARG121 3.7 10.0 1.0
CD2 B:HIS56 3.8 6.8 1.0
C B:GLN81 3.8 7.9 1.0
N B:THR82 3.8 7.9 1.0
CA B:THR82 3.8 7.1 1.0
C B:THR82 3.9 7.5 1.0
CE1 B:TYR306 4.0 8.1 1.0
N B:TYR83 4.1 7.4 1.0
CD2 B:TYR83 4.1 8.0 1.0
CD1 B:TYR306 4.1 8.3 1.0
CD B:GLN81 4.2 9.5 1.0
CB B:GLN81 4.3 8.4 1.0
CE2 B:TYR83 4.3 8.2 1.0
O B:THR82 4.4 7.8 1.0
CG B:TYR83 4.4 7.8 1.0
CA B:SER54 4.4 8.5 1.0
CE1 B:HIS56 4.4 7.2 1.0
CD B:ARG121 4.6 9.8 1.0
CZ B:TYR83 4.6 8.6 1.0
CA B:GLN81 4.7 8.4 1.0
CD1 B:TYR83 4.8 7.6 1.0
CG B:ARG121 4.8 9.6 1.0
CE1 B:TYR83 4.9 8.5 1.0
ND2 B:ASN304 5.0 8.6 1.0
CA B:TYR83 5.0 7.1 1.0
CB B:TYR83 5.0 7.3 1.0

Chlorine binding site 3 out of 4 in 3thd

Go back to Chlorine Binding Sites List in 3thd
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl801

b:6.2
occ:1.00
 OG C:SER54 3.1 10.3 1.0
NE2 C:HIS56 3.2 8.6 1.0
NH2 C:ARG121 3.3 9.6 1.0
NE C:ARG121 3.5 9.8 1.0
CB C:SER54 3.6 9.4 1.0
CG C:GLN81 3.7 9.6 1.0
O C:GLN81 3.7 10.0 1.0
NE2 C:GLN81 3.7 9.1 1.0
CD2 C:HIS56 3.7 8.0 1.0
C C:GLN81 3.8 9.9 1.0
N C:THR82 3.8 9.9 1.0
CZ C:ARG121 3.8 9.9 1.0
CA C:THR82 3.8 9.8 1.0
C C:THR82 4.0 10.4 1.0
CE1 C:TYR306 4.0 9.2 1.0
CD2 C:TYR83 4.1 9.8 1.0
CB C:GLN81 4.2 9.5 1.0
CD1 C:TYR306 4.2 9.9 1.0
N C:TYR83 4.2 10.4 1.0
CD C:GLN81 4.2 9.5 1.0
CE2 C:TYR83 4.2 9.4 1.0
CE1 C:HIS56 4.4 8.3 1.0
CG C:TYR83 4.4 9.9 1.0
CA C:SER54 4.4 9.3 1.0
O C:THR82 4.5 11.3 1.0
CA C:GLN81 4.6 10.0 1.0
CZ C:TYR83 4.7 9.7 1.0
CD C:ARG121 4.7 10.2 1.0
CD1 C:TYR83 4.8 9.6 1.0
CG C:ARG121 4.9 10.1 1.0
CE1 C:TYR83 4.9 9.8 1.0
ND2 C:ASN304 4.9 9.2 1.0

Chlorine binding site 4 out of 4 in 3thd

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Chlorine binding site 4 out of 4 in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl801

b:6.0
occ:1.00
 OG D:SER54 3.0 10.6 1.0
NH2 D:ARG121 3.2 10.0 1.0
NE2 D:HIS56 3.2 10.6 1.0
NE D:ARG121 3.5 10.4 1.0
O D:GLN81 3.6 9.0 1.0
CB D:SER54 3.7 9.7 1.0
CZ D:ARG121 3.8 10.6 1.0
NE2 D:GLN81 3.8 9.8 1.0
CG D:GLN81 3.8 9.4 1.0
CD2 D:HIS56 3.8 10.2 1.0
C D:GLN81 3.8 8.9 1.0
N D:THR82 3.9 8.8 1.0
CA D:THR82 3.9 9.2 1.0
CE1 D:TYR306 3.9 9.9 1.0
C D:THR82 4.1 9.5 1.0
CD2 D:TYR83 4.1 9.9 1.0
CD1 D:TYR306 4.1 10.4 1.0
CE2 D:TYR83 4.2 10.1 1.0
N D:TYR83 4.2 9.7 1.0
CB D:GLN81 4.2 9.5 1.0
CD D:GLN81 4.3 9.8 1.0
CG D:TYR83 4.4 10.2 1.0
CE1 D:HIS56 4.4 10.8 1.0
CA D:SER54 4.4 9.7 1.0
CZ D:TYR83 4.6 10.0 1.0
O D:THR82 4.6 10.1 1.0
CD D:ARG121 4.7 11.8 1.0
CA D:GLN81 4.7 9.2 1.0
CD1 D:TYR83 4.8 10.0 1.0
CE1 D:TYR83 4.9 10.1 1.0
ND2 D:ASN304 4.9 12.0 1.0

Reference:

U.Ohto, K.Usui, T.Ochi, K.Yuki, Y.Satow, T.Shimizu. Crystal Structure of Human Beta-Galactosidase: Structural Basis of GM1 Gangliosidosis and Morquio B Diseases J.Biol.Chem. V. 287 1801 2012.
ISSN: ISSN 0021-9258
PubMed: 22128166
DOI: 10.1074/JBC.M111.293795
Page generated: Fri Jul 11 10:44:07 2025

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